Autoimmune Diseases and Pregnancy - What to Expect When You’re TTC

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14 minute read Updated on 16th April 2025

Autoimmune Diseases and Pregnancy - What to Expect When You’re TTC

Written by Haley Fritz
Medically reviewed by Banafsheh Kashani, MD, FACOG

Understanding Autoimmune Diseases and Pregnancy

Of all the people diagnosed with an autoimmune disorder, approximately 80% are women. 

Research shows symptoms and flare-ups often peak during a woman’s reproductive years. Naturally, this can have widespread implications for fertility and pregnancy. 

The key thing to remember is that most women with an autoimmune disease go on to have a healthy pregnancy. However, specialist planning and care are often required to protect the health of both mother and baby. 

Read on to learn how different autoimmune disorders affect fertility and what you can do to prepare for a healthy pregnancy. 

Autoimmune Diseases Explained

The immune system is designed to defend the body from foreign ‘invaders’ — such as bacteria, germs, and viruses that can make us sick. 

But if you have an autoimmune disease, your body confuses its own cells with foreign cells. This confusion causes the body to ‘attack’ its own healthy cells instead of allowing them to function the way they’re supposed to. This leads to inflammation, tissue damage, and a whole host of uncomfortable symptoms. 

How Autoimmune Diseases Affect Fertility

In general, autoimmune diseases can impact fertility in three key ways: 

  • Inflammation. Chronic inflammation due to an autoimmune disorder can interfere with ovarian functioning and reduce ovarian reserve in some cases. 

  • Hormone Imbalance. Certain autoimmune disorders can lead to hormone imbalance, which may disrupt or prevent ovulation. 

  • Conception and Pregnancy Risks. Certain autoimmune disorders are linked with an increased risk of implantation failure, miscarriage, and recurrent miscarriage. 

It’s important to note that there are over 80 different types of autoimmune diseases. Some impact fertility and pregnancy, others do not. When navigating an autoimmune disease and pregnancy, make sure to always consult your doctor about any risks related to your specific condition. 

 


Planning for Pregnancy With an Autoimmune Disease

When Is the Best Time to Get Pregnant?

The standard guideline is to achieve remission for at least six months before starting the TTC process. This can help reduce the overall risk of pregnancy complications. 

Preconception Checklist

If you’ve been diagnosed with an autoimmune disorder, the following checklist can help you plan a pregnancy safely: 

  • Notify your doctor about your desire to plan a pregnancy.

  • Ask your doctor if any of your current medications need to be adjusted ahead of and/or during pregnancy.

  • Consult with a relevant specialist, such as a rheumatologist, endocrinologist, or perinatologist (sometimes referred to as an MFM doctor).

  • Attend regular check-ups to monitor the progress of your condition.

  • Embrace a healthy pre-pregnancy diet and lifestyle. 

  • Take a prenatal multi-vitamin to equip your body for pregnancy. 

  • Start tracking your cycle and ovulation patterns. Fertility tracking tools (like the Mira App and Hormone Monitor) can help with this.

  • Consider PCOS supplements to support hormone balance and cycle regularity. 

Common Autoimmune Diseases and Their Impact on Pregnancy

Systemic Lupus Erythematosus (SLE) and Pregnancy

Systemic lupus erythematosus, known as SLE or just ‘lupus’ for short, is an autoimmune disease that causes inflammation in the connective tissues of the body. 

With lupus, antibodies can cross the placenta during pregnancy. This can increase the risk of: 

  • Miscarriage

  • Preeclampsia

  • Stillbirth

Doctors recommend achieving remission for at least six months before planning a pregnancy with lupus.  

Rheumatoid Arthritis (RA) and Pregnancy

Rheumatoid arthritis or RA is an autoimmune disease where the immune system attacks the joints. 

For expectant mothers, research suggests RA can increase the risk of:

  • Preeclampsia

  • Gestational diabetes

  • Spontaneous abortion

  • Cesarean delivery

  • Stillbirth

For infants, RA can increase the risk of:

  • Congenital abnormalities

  • Small for gestational age 

  • Low birth weight 

  • Type 1 diabetes

  • Asthma 

Doctors recommend achieving remission for at least six months before planning a pregnancy with RA. 

During pregnancy, you may notice an improvement in RA symptoms. Here’s why:

  • The body’s immune system while pregnant makes a natural shift to an anti-inflammatory state, helping to prevent the body from rejecting the developing embryo or fetus. 

  • Elevated estrogen and progesterone levels during pregnancy can also have an anti-inflammatory effect on the body. 

After pregnancy, RA symptoms are likely to return as hormones settle back to their baseline levels. 

Antiphospholipid Syndrome (APS) and Pregnancy

Antiphospholipid Syndrome, known as APS or Hughes Syndrome is a type of autoimmune disorder that increases the risk of blood clots. 

During pregnancy, APS may cause blood clots to form in the placenta, resulting in reduced blood supply to a developing fetus. This can increase the risk of: 

  • Recurrent pregnancy loss

  • Preterm delivery

  • Preeclampsia

  • Placental abruption

  • Stillbirth

APS is often treated with aspirin or heparin during pregnancy. This can help improve pregnancy outcomes, with research suggesting the live birth rate improves from 50% to 85% when APS is treated.

Hashimoto’s and Graves’ Disease (Thyroid Autoimmune Diseases)

The thyroid is a butterfly-shaped gland that produces thyroid hormones. Thyroid hormones help regulate key processes and systems in the body, such as the: 

  • Metabolism

  • Nervous system

  • Reproductive system 

With Hashimoto’s disease, the thyroid is ‘underactive’. This means it produces fewer thyroid hormones than it is supposed to. With Graves’ disease, the thyroid is ‘overactive’. This means it produces too many thyroid hormones.

During pregnancy, thyroid hormones support brain and nervous system development. If thyroid hormones are out of balance, this can increase the risk of: 

  • Miscarriage

  • Preeclampsia

  • Premature birth

  • Low birth weight

  • Stillbirth

Thyroid functioning should be closely monitored during pregnancy, especially if you have a history of thyroid disease or if you experience any symptoms of over/underactive thyroid.

Myasthenia Gravis (MG) and Pregnancy

Myasthenia gravis or MG is a rare autoimmune condition where the body destroys connections between the muscles and nerves. 

During pregnancy, MG increases the risk of:

  • Muscle weakness 

  • Preterm delivery

  • Difficult delivery 

After delivery, infants born to mothers with MG are at risk of having neonatal myasthenia gravis (TNMG). This is a temporary disorder that may lead to the following symptoms:

  • Weak ‘floppy’ muscles

  • Weak suck, making it difficult to breastfeed

  • Breathing difficulties 

Any baby born to a mother with MG will need to be closely monitored for at least three days following delivery. Most symptoms go away within a few weeks or months, with TNMG rarely leading to life-threatening complications when identified and treated. 

Sjögren’s Syndrome and Pregnancy

Sjögren’s syndrome is an autoimmune condition that interrupts fluid-producing glands, such as the glands that produce tears, sweat, and spit. 

During pregnancy, research suggests Sjögren’s may increase the risk of spontaneous abortion. Infants are also at risk of neonatal lupus and congenital heart block, due to the high prevalence of anti-SS-A and anti-SS-B antibodies in pregnant mothers with Sjögren’s.  

Scleroderma and Pregnancy

Scleroderma is an autoimmune condition that affects connective tissues in the skin and internal organs. Mild cases of scleroderma only affect localized areas of the body. Severe or ‘systemic’ scleroderma can affect the entire body. 

With systemic scleroderma, there is an increased risk of kidney failure and high blood pressure during pregnancy. This can increase the risk of: 

  • First-trimester miscarriage

  • Preeclampsia

  • Small for gestational age

  • Preterm delivery

Doctors recommend achieving remission for at least six months before planning a pregnancy with systemic scleroderma. 

Autoimmune Disorders and Pregnancy: Monitoring Your Risks and Planning for Delivery

What Tests Should I Get Before Pregnancy?

In a basic pre-pregnancy health checkup, your doctor will evaluate the following:

  • Overall health (weight, nutrition, lifestyle, medical history, and medications)

  • Vaccination status

  • Gynecological health and history, including a cervical screening and STI (sexually transmitted infection) testing

Your doctor will also likely run basic blood tests to screen for:

  • Anemia

  • Rubella immunity

  • Chickenpox immunity 

To get a general idea of your overall reproductive health and fertility before planning a pregnancy, you can also take Mira’s Panorama Lab Test. This is an at-home test that can provide insight into your ovarian reserve, cycle regularity, and hormone balance. This information can help you make informed choices ahead of your TTC journey. 

If you have a history of autoimmune disease, or if you have had three or more miscarriages, you will likely need advanced testing at your doctor’s office to check for:

  • Autoantibodies and inflammatory markers

  • Thyroid functioning and hormone balance

  • Blood clotting disorders

  • Genetic disorders

These tests can help your doctor assess whether or not a potential autoimmune disease (or other condition) may interfere with your body’s ability to maintain a healthy pregnancy. Your doctor can then provide you with an appropriate treatment strategy that’s aligned with your pregnancy goals. 

How Are Autoimmune Disorders Monitored During Pregnancy?

If you become pregnant with an autoimmune disorder, your doctor will want to keep a close eye on your pregnancy. This may involve additional monitoring, such as:

  • Adjusting your medication so that it’s pregnancy-friendly. 

  • Regular blood testing to monitor inflammatory markers, such as elevated WBC (white blood cell) count in pregnancy.

  • Advanced fetal monitoring to identify potential complications as soon as possible.

The impact an autoimmune disease can have on a pregnancy depends on the type of disease, the severity of the disease, and your medical history. If you are navigating a pregnancy alongside an autoimmune disorder, make sure to follow your doctor’s personalized recommendations closely. This is the best way to safeguard your own health and the health of your baby. 

What Should I Expect During and After Delivery?

Depending on the type and severity of your condition, you may need to create a specialized birth plan with your doctor. A birth plan can take your pain levels, medications, and preferences into consideration to ensure everyone’s on the same page ahead of delivery. 

If you experienced relief from your symptoms during pregnancy, you may notice symptoms return in the weeks and months following birth. This is normal, and your doctor may need to adjust your medications to address any symptom changes after pregnancy.

Medications and Supplements for Autoimmune Diseases in Pregnancy

Autoimmune Disease and Pregnancy: Medications and Supplements

Condition

Safe While TTC and Pregnant

Not Safe While TTC and Pregnant

Systemic Lupus Erythematosus (SLE)

Hydroxychloroquine

Methotrexate

Rheumatoid Arthritis (RA)

Hydroxychloroquine

Sulfasalazine

Methotrexate 

Leflunomide

Antiphospholipid Syndrome (APS)

Aspirin

Heparin

Warfarin

Hashimoto’s Disease

Levothyroxine

PCOS Supplements

Methimazole

Graves’ Disease

Propylthiouracil 

PCOS Supplements

Methimazole

Myasthenia Gravis

Pyridostigmine Corticosteroids (in low doses) Azathioprine

Mycophenolate mofetil

Methotrexate

Cyclophosphamide

Magnesium (may trigger flare-ups)

Sjögren’s Syndrome

Hydroxychloroquine

Methotrexate

Cyclophosphamide

Scleroderma

Corticosteroids

Methotrexate

Cyclophosphamide

Mycophenolate mofetil

Thalidomide

 

Please note the above table is for informational purposes only. Always seek specialist guidance from your doctor regarding suitable medications while TTC, during pregnancy, and when breastfeeding. 

Final Thoughts

It is possible to have a healthy pregnancy with an autoimmune disease. However, it does require careful planning and medical supervision. 

If you have been diagnosed with an autoimmune disease and want to plan a pregnancy, seek pre-pregnancy counseling from your doctor. They can adjust your medication and provide guidance on the best way to plan a pregnancy with minimal risk to yourself and your baby. 

You should also speak with your doctor if you have experienced three miscarriages in a row. Your doctor can run advanced blood testing and screenings to assess whether or not an underlying autoimmune condition could be interfering with your ability to maintain a pregnancy. They can also advise on treatment options that can help reduce your risk of miscarriage in the future. 

Frequently Asked Questions

Can I get pregnant if I have an autoimmune disease?

Yes. You can get pregnant even if you have an autoimmune disease. However, you should let your doctor know that you want to plan a pregnancy so that you get appropriate treatment ahead of and during pregnancy. 

Which autoimmune diseases affect fertility the most?

Lupus, antiphospholipid syndrome (APS), rheumatoid arthritis (RA), and Hashimoto’s disease are the most common autoimmune diseases that can affect fertility. 

What are the safest medications for pregnancy?

Hydroxychloroquine, heparin, and levothyroxine are three common medications used to treat autoimmune disorders that are also safe for pregnancy. Always consult your doctor for personalized guidance on which medications are safe to take during pregnancy. 

Can I pass my autoimmune disease to my baby?

In the short term, yes. Certain autoimmune diseases (such as neonatal myasthenia gravis) can be temporarily passed on to an infant. However, symptoms are typically resolved within a few weeks or months, with no long-term risk. 

How do I reduce pregnancy risks if I have lupus or APS?

The best way to reduce your pregnancy risks with lupus, APS, or any autoimmunity condition in pregnancy is by:

  • Waiting to conceive until you have achieved remission for at least six months

  • Attending all prenatal appointments and checkups

  • Following your doctor’s guidance on any medication or lifestyle adjustments

Can I breastfeed while taking autoimmune medications?

Most autoimmune medications can be taken while breastfeeding. Make sure to speak with your doctor if you have any concerns about a specific medication and its compatibility with breastfeeding.

What are the most common pregnancy autoimmune disorders?

Some of the most common autoimmune disorders seen in pregnancy include systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), antiphospholipid syndrome (APS), Hashimoto’s disease, Graves’ disease, Sjögren’s syndrome, myasthenia gravis, and scleroderma. 

Are autoimmune disorders and miscarriage related?

Yes, autoimmune diseases and miscarriage are linked. However, the risk of miscarriage depends on the type of autoimmune disease, the severity of the disease, and your individual medical history. 

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